Two PCR methods were developed for specific detection of the trnS-trnG intergenic spacer region of Prunus persica (peach) and the internal transcribed spacer region of Malus domestica (apple). The peach PCR amplified a target-size product from DNA of six Prunus persica cultivars including two nectarine and one flat peach cultivars, but not from those of 36 nontarget species including six Prunus and five other Rosaceae species. The apple PCR amplified a target-size product from DNAs of five Malus domestica cultivars, but not from those of 41 nontarget species including seven Maloideae and nine other Rosaceae species. Both methods detected the target DNA from strawberry jam and cookies spiked with peach and apple at a level equivalent to about 10 g total soluble proteins of peach or apple/g incurred food. These specificity and sensitivity were considered sufficient for detection of trace amounts of peach or apple contamination in processed foods.